Re: [yt-users] Error while using annotate magnetic fields

16 Mar 2016

      Hi Sushil,

I think so — here is an example of 3D streamline with mplot3d: http://yt-project.org/docs/dev/cookbook/complex_plots.html#plotting-streamli... http://yt-project.org/docs/dev/cookbook/complex_plots.html#plotting-streamli..., and you could modify it for quiver plotting by adopting this example: http://matplotlib.org/examples/mplot3d/quiver3d_demo.html http://matplotlib.org/examples/mplot3d/quiver3d_demo.html

Best wishes,
--
Suoqing JI
Ph.D Candidate
Department of Physics
University of California, Santa Barbara
http://web.physics.ucsb.edu/~suoqing
...
On Mar 16, 2016, at 1:56 PM, Sushilkumar  wrote:
Dear Suoqing Ji and yt:
Thank you for your help. It worked
In addition, does yt support 3D quiver plots?
If not what is the equivalent for visualizing 3d magnetic fields.
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Today's Topics:
1. Error while using annotate magnetic fields (Sushilkumar)
   2. Re: Error while using annotate magnetic fields (Suoqing Ji)
----------------------------------------------------------------------
Message: 1
Date: Wed, 16 Mar 2016 14:16:37 -0500
From: Sushilkumar mailto:sushil.sush19us@gmail.com>
To: Discussion of the yt analysis package
        mailto:yt-users@lists.spacepope.org>
Subject: [yt-users] Error while using annotate magnetic fields
Message-ID:
        mailto:CAKARaKWgFBsh7qZj8Px%2BOS0-tDUOuKcv2MrWyJh3NaGtj06-9g@mail.gmail.com>
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Dear yt:
I am trying to plot magnetic field lines using the annotate magnetic field
call back from the link http://yt-project.org/doc/visualizing/callbacks.html http://yt-project.org/doc/visualizing/callbacks.html
link.
However, after running the script it gives the error below. A google drive
link to my script (yt_numpy_load_B.py) is also given below. When I use
quiver annotate it works fine but issue comes when I am using
slc.annotate_magnetic_field().
Quiver plots are also available on the drive link.
Thanks in advance
===============
Google drive link
https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc
===============
===============
Error while running the script
File "yt_numpy_load_B.py", line 47, in <module>
    slc.save()
  File
"/state/partition1/anaconda/lib/python2.7/site-packages/yt/visualization/plot_container.py",
line 77, in newfunc
    args[0]._setup_plots()
  File
"/state/partition1/anaconda/lib/python2.7/site-packages/yt/visualization/plot_window.py",
line 980, in _setup_plots
    self.run_callbacks()
  File
"/state/partition1/anaconda/lib/python2.7/site-packages/yt/visualization/plot_window.py",
line 1033, in run_callbacks
    sys.exc_info()[2])
  File
"/state/partition1/anaconda/lib/python2.7/site-packages/yt/visualization/plot_window.py",
line 1029, in run_callbacks
    callback(cbw)
  File
"/state/partition1/anaconda/lib/python2.7/site-packages/yt/visualization/plot_modifications.py",
line 316, in __call__
    return qcb(plot)
  File
"/state/partition1/anaconda/lib/python2.7/site-packages/yt/visualization/plot_modifications.py",
line 357, in __call__
    fv_x = plot.data[self.field_x]
  File
"/state/partition1/anaconda/lib/python2.7/site-packages/yt/data_objects/data_containers.py",
line 246, in __getitem__
    f = self._determine_fields([key])[0]
  File
"/state/partition1/anaconda/lib/python2.7/site-packages/yt/data_objects/data_containers.py",
line 518, in _determine_fields
    finfo = self.ds._get_field_info("unknown", fname)
  File
"/state/partition1/anaconda/lib/python2.7/site-packages/yt/data_objects/static_output.py",
line 543, in _get_field_info
    raise YTFieldNotFound((ftype, fname), self)
yt.utilities.exceptions.YTPlotCallbackError: annotate_magnetic_field
callback failed with the following error: Could not find field '('all',
'magnetic_field_x')' in UniformGridData.
===============
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Today's Topics:
1. Re: Making averaged line plot. (Suoqing Ji)
----------------------------------------------------------------------
Message: 1
Date: Tue, 15 Mar 2016 15:23:43 -0700
From: Suoqing Ji mailto:suoqing@physics.ucsb.edu>
To: Discussion of the yt analysis package
        mailto:yt-users@lists.spacepope.org>
Subject: Re: [yt-users] Making averaged line plot.
Message-ID: <70E5BA6C-7798-45F2-AE83-21233252E109@physics.ucsb.edu mailto:70E5BA6C-7798-45F2-AE83-21233252E109@physics.ucsb.edu>
Content-Type: text/plain; charset="utf-8"
Hi Yuxiao,
If you would like to start from your current code, the most
straightforward way is to write a loop to smooth over a certain distance by
each step, which also works for AMR data:
smooth_len = 100 # smoothing length of 100 kpc
SmoothedBMag = np.copy(ray[?ScaledBMag?]) # store the smoothed array
bin_num = np.ceiling((ray[?x?].max() - ray[?x?].min()) / smooth_len) #
make bins every 100 kpc
for step in range(bin_num):
    mask1 = (ray[?x?] >= ray[?x?].min() + step * smooth_len)
    mask2 = (ray[?x?] < ray[?x?].min() + (step + 1) * smooth_len)
    mask = np.logical_and(mask1, mask2) # mask the cells within a certain
length of 100 kpc
    SmoothedBMag[mask] = np.mean(ray[?ScaledBMag?][mask]) # take the
average and save
After that the array ?SmoothedBMag? is the smoothed one.
However, an easier way is to use the the 1D ProfilePlot function (
http://yt-project.org/docs/2.6/visualizing/plots.html#d-profile-plots http://yt-project.org/docs/2.6/visualizing/plots.html#d-profile-plots <
http://yt-project.org/docs/2.6/visualizing/plots.html#d-profile-plots http://yt-project.org/docs/2.6/visualizing/plots.html#d-profile-plots>),
and in this case you could do something like:
plot = ProfilePlot(pf.h.all_data(), ?x?, [?ScaledBMag?], n_bins=bin_num)
Note that this will do the average over entire y-z plane for each x bins,
which is different from averaging only an array of a ray object (so maybe
it?s not what you want). If you really want the data within a thin slit
only, you could define a region object pf.h.region() and do ProfilePlot. I
think it?s also doable to use the function ?load_uniform_grid? to create a
1D dataset from the arrays in ray object and pass it to ProfilePlot.
Best wishes,
--
Suoqing JI
Ph.D Candidate
Department of Physics
University of California, Santa Barbara
http://web.physics.ucsb.edu/~suoqing http://web.physics.ucsb.edu/~suoqing
...
On Mar 14, 2016, at 10:57 PM, Yuxiao Dai mailto:yuxiao.dai@nyu.edu> wrote:
Dear all,
I have a line plot of some parameter along an axis as a function of
distance. Now I would like to get another line plot of the same parameter
but averaged over a certain distance (say 100 kpc, the plot below is
supposed to be flat after this). I've been searching the document for some
time but haven't found a method. Is there a simple way to do this?
I would very much appreciate it if anyone could help me on this.
===================================
import ...
def _ScaledBMag(field, data):
return ...
....
pf = load(filename)
add_field("ScaledBMag", function=_ScaledBMag)
c = pf.h.find_max('ScaledBMag')[1]
ax = 0
ray = pf.h.ortho_ray(ax, (c[1], c[2]))
P.subplot(211)
P.semilogy(ray['x'], ray['ScaledBMag'])
P.xlabel('x')
P.ylabel('ScaledBMag')
print "works"
P.savefig("ScaledBMag_lineplot.png")

===================================
I'm using yt
Version = 2.6.1
Changeset = c994959ed3be
===================================
Regards,
Dai
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Message: 2
Date: Wed, 16 Mar 2016 12:49:09 -0700
From: Suoqing Ji mailto:suoqing@physics.ucsb.edu>
To: Discussion of the yt analysis package
        mailto:yt-users@lists.spacepope.org>
Subject: Re: [yt-users] Error while using annotate magnetic fields
Message-ID: <9CA99B80-FF30-44F0-B8C8-74EBC0A4E3CA@physics.ucsb.edu mailto:9CA99B80-FF30-44F0-B8C8-74EBC0A4E3CA@physics.ucsb.edu>
Content-Type: text/plain; charset="utf-8"
Hi Sushil,
I think what you need to do is to assign the correct field name when loading the data. In your script, you have:
data = dict(field1 = field1,
            field2 = field2,
            field3 = field3)
which could be, say,
data = dict(magnetic_field_x = field1,
            magnetic_field_y = field2,
            magnetic_field_z = field3)
since annotate_magnetic_field will directly refer to these field names (in fact it's a specialized version of annotate_quiver).
Best wishes,
--
Suoqing JI
Ph.D Candidate
Department of Physics
University of California, Santa Barbara
http://web.physics.ucsb.edu/~suoqing http://web.physics.ucsb.edu/~suoqing
...
On Mar 16, 2016, at 12:16 PM, Sushilkumar mailto:sushil.sush19us@gmail.com> wrote:
Dear yt:
I am trying to plot magnetic field lines using the annotate magnetic field call back from the link http://yt-project.org/doc/visualizing/callbacks.html http://yt-project.org/doc/visualizing/callbacks.html <http://yt-project.org/doc/visualizing/callbacks.html http://yt-project.org/doc/visualizing/callbacks.html> link.
However, after running the script it gives the error below. A google drive link to my script (yt_numpy_load_B.py) is also given below. When I use quiver annotate it works fine but issue comes when I am using slc.annotate_magnetic_field().
Quiver plots are also available on the drive link.
Thanks in advance
===============
Google drive link
https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc <https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc>
===============
===============
Error while running the script
File "yt_numpy_load_B.py", line 47, in <module>
    slc.save()
  File "/state/partition1/anaconda/lib/python2.7/site-packages/yt/visualization/plot_container.py", line 77, in newfunc
    args[0]._setup_plots()
  File "/state/partition1/anaconda/lib/python2.7/site-packages/yt/visualization/plot_window.py", line 980, in _setup_plots
    self.run_callbacks()
  File "/state/partition1/anaconda/lib/python2.7/site-packages/yt/visualization/plot_window.py", line 1033, in run_callbacks
    sys.exc_info()[2])
  File "/state/partition1/anaconda/lib/python2.7/site-packages/yt/visualization/plot_window.py", line 1029, in run_callbacks
    callback(cbw)
  File "/state/partition1/anaconda/lib/python2.7/site-packages/yt/visualization/plot_modifications.py", line 316, in __call__
    return qcb(plot)
  File "/state/partition1/anaconda/lib/python2.7/site-packages/yt/visualization/plot_modifications.py", line 357, in __call__
    fv_x = plot.data[self.field_x]
  File "/state/partition1/anaconda/lib/python2.7/site-packages/yt/data_objects/data_containers.py", line 246, in __getitem__
    f = self._determine_fields([key])[0]
  File "/state/partition1/anaconda/lib/python2.7/site-packages/yt/data_objects/data_containers.py", line 518, in _determine_fields
    finfo = self.ds._get_field_info("unknown", fname)
  File "/state/partition1/anaconda/lib/python2.7/site-packages/yt/data_objects/static_output.py", line 543, in _get_field_info
    raise YTFieldNotFound((ftype, fname), self)
yt.utilities.exceptions.YTPlotCallbackError: annotate_magnetic_field callback failed with the following error: Could not find field '('all', 'magnetic_field_x')' in UniformGridData.
===============
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Today's Topics:
1. Re: Making averaged line plot. (Suoqing Ji)
----------------------------------------------------------------------
Message: 1
Date: Tue, 15 Mar 2016 15:23:43 -0700
From: Suoqing Ji mailto:suoqing@physics.ucsb.edu mailto:suoqing@physics.ucsb.edu>>
To: Discussion of the yt analysis package
        mailto:yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org>>
Subject: Re: [yt-users] Making averaged line plot.
Message-ID: <70E5BA6C-7798-45F2-AE83-21233252E109@physics.ucsb.edu mailto:70E5BA6C-7798-45F2-AE83-21233252E109@physics.ucsb.edu mailto:70E5BA6C-7798-45F2-AE83-21233252E109@physics.ucsb.edu>>
Content-Type: text/plain; charset="utf-8"
Hi Yuxiao,
If you would like to start from your current code, the most straightforward way is to write a loop to smooth over a certain distance by each step, which also works for AMR data:
smooth_len = 100 # smoothing length of 100 kpc
SmoothedBMag = np.copy(ray[?ScaledBMag?]) # store the smoothed array
bin_num = np.ceiling((ray[?x?].max() - ray[?x?].min()) / smooth_len) # make bins every 100 kpc
for step in range(bin_num):
    mask1 = (ray[?x?] >= ray[?x?].min() + step * smooth_len)
    mask2 = (ray[?x?] < ray[?x?].min() + (step + 1) * smooth_len)
    mask = np.logical_and(mask1, mask2) # mask the cells within a certain length of 100 kpc
    SmoothedBMag[mask] = np.mean(ray[?ScaledBMag?][mask]) # take the average and save
After that the array ?SmoothedBMag? is the smoothed one.
However, an easier way is to use the the 1D ProfilePlot function (http://yt-project.org/docs/2.6/visualizing/plots.html#d-profile-plots http://yt-project.org/docs/2.6/visualizing/plots.html#d-profile-plots <http://yt-project.org/docs/2.6/visualizing/plots.html#d-profile-plots http://yt-project.org/docs/2.6/visualizing/plots.html#d-profile-plots> <http://yt-project.org/docs/2.6/visualizing/plots.html#d-profile-plots http://yt-project.org/docs/2.6/visualizing/plots.html#d-profile-plots <http://yt-project.org/docs/2.6/visualizing/plots.html#d-profile-plots http://yt-project.org/docs/2.6/visualizing/plots.html#d-profile-plots>>), and in this case you could do something like:
plot = ProfilePlot(pf.h.all_data(), ?x?, [?ScaledBMag?], n_bins=bin_num)
Note that this will do the average over entire y-z plane for each x bins, which is different from averaging only an array of a ray object (so maybe it?s not what you want). If you really want the data within a thin slit only, you could define a region object pf.h.region() and do ProfilePlot. I think it?s also doable to use the function ?load_uniform_grid? to create a 1D dataset from the arrays in ray object and pass it to ProfilePlot.
Best wishes,
--
Suoqing JI
Ph.D Candidate
Department of Physics
University of California, Santa Barbara
http://web.physics.ucsb.edu/~suoqing http://web.physics.ucsb.edu/~suoqing <http://web.physics.ucsb.edu/~suoqing http://web.physics.ucsb.edu/~suoqing>
...
On Mar 14, 2016, at 10:57 PM, Yuxiao Dai mailto:yuxiao.dai@nyu.edu mailto:yuxiao.dai@nyu.edu>> wrote:
Dear all,
I have a line plot of some parameter along an axis as a function of distance. Now I would like to get another line plot of the same parameter but averaged over a certain distance (say 100 kpc, the plot below is supposed to be flat after this). I've been searching the document for some time but haven't found a method. Is there a simple way to do this?
I would very much appreciate it if anyone could help me on this.
===================================
import ...
def _ScaledBMag(field, data):
return ...
....
pf = load(filename)
add_field("ScaledBMag", function=_ScaledBMag)
c = pf.h.find_max('ScaledBMag')[1]
ax = 0
ray = pf.h.ortho_ray(ax, (c[1], c[2]))
P.subplot(211)
P.semilogy(ray['x'], ray['ScaledBMag'])
P.xlabel('x')
P.ylabel('ScaledBMag')
print "works"
P.savefig("ScaledBMag_lineplot.png")

===================================
I'm using yt
Version = 2.6.1
Changeset = c994959ed3be
===================================
Regards,
Dai
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****************************************
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"Claiming that something can move faster than light is a good conversation-stopper in physics. People edge away from you in cocktail parties; friends never return phone calls. You just don?t mess with Albert Einstein."
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